_targets.R

# === Extended {targets} pipeline -----------------------------------------
# Alec L. Robitaille, Isabella C. Richmond



# Source ------------------------------------------------------------------
library(targets)
tar_source('R')



# Variables ---------------------------------------------------------------
# File paths
path_counts <- file.path('raw-data', 'adelie-adult-chick-counts.csv')
path_ice <- file.path('raw-data', 'ice-area.txt')
path_weather <- file.path('raw-data', 'weather-timeseries.csv')

# Column names
x_col <- 'date_gmt'
y_col <- 'adults'
color_col <- 'colony'

# Directories
dir_output <- 'output'
dir_figures <- 'figures'

if (!dir.exists(dir_output)) dir.create(dir_output)
if (!dir.exists(dir_figures)) dir.create(dir_figures)

# Filters
filter_year <- 1995



# Targets -----------------------------------------------------------------
c(
    # Files
    tar_target(
        file_counts,
        path_counts,
        format = 'file'
    ),
    tar_target(
        file_weather,
        path_weather,
        format = 'file'
    ),


    # Prepare
    tar_target(
        prep_counts,
        prepare_csv(file_counts)
    ),
    tar_target(
        prep_weather,
        prepare_csv(file_weather)
    ),

    # Sum counts
    tar_target(
        sums,
        sum_counts(prep_counts, 'island')
    ),

    # Filter
    tar_target(
        filter_counts,
        filter(prep_counts, year(date_gmt) > filter_year)
    ),

    # Group
    tar_group_by(
        group_counts,
        filter_counts,
        island
    ),

    # Keys for groups
    tar_target(
        group_keys,
        unique(group_counts$island),
        pattern = map(group_counts)
    ),

    # Plot by group
    tar_target(
        plot_groups,
        plot_xy(group_counts, x_col, y_col, color_col) + ggtitle(group_keys),
        pattern = map(group_counts, group_keys),
        iteration = 'list'
    ),

    # Save plots
    tar_target(
        save_plots,
        ggsave(filename = paste0(file.path(dir_figures, group_keys), '.png'),
               plot = plot_groups),
        pattern = map(plot_groups, group_keys),
        format = 'file'
    ),

    # Model by group
    tar_target(
        model_adult_groups,
        lm(adults ~ date_gmt + (colony), data = group_counts),
        pattern = map(group_counts),
        iteration = 'list'
    ),
    tar_target(
        model_chicks_groups,
        lm(chicks ~ date_gmt + (colony), data = group_counts),
        pattern = map(group_counts),
        iteration = 'list'
    ),

    # Write tables
    tar_target(
        save_tables,
        fwrite(sums, file.path(dir_output, 'sums.csv')),
        format = 'file'
    ), 
    
    # Manuscript
    tar_quarto(
        render,
        file.path('paper', 'manuscript.qmd')
    )

)